The occurrence and significance of autoimmune manifestations after administration of vaccines remain controversial. Evidence for immunization triggered autoimmunity come from several sources including theoretical models, animal studies, single and multiple case reports. In contrast, several epidemiological studies don’t report this association, which is reassuring and at least indicates that vaccines are not a major cause of autoimmune diseases. We analyzed current scientific data concluded that vaccines bring a positive impact on public health, so it is necessary to continue developing this technology. Evaluation methods should be improved to avoid or anticipate the possible autoimmune side effects that can be presented.